Dan, can you please try exporting the file to pvz format (in creo illustrate) and see if the problem persist.
Also as a workaround, the color of the 3D model can also be changed from Thingworx Studio. Please follow the article - How to change color of the 3D model in TWX Studio
Let me know if that works,
There is no option to "export" or "save as" a pvz in Creo Illustrate that I am aware of. When I click on FILE and then PUBLISH, I am able to save it as a pvz. That is what I did.
Changing the color using Model Item is not a good option because I would have more than 150 Model Items.
There must be a setting or some option within Creo Illustrate to make the colors stick. It worked for me in the past, but I'm not sure what has changed.